rs202032297
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP2BP4_StrongBP6BS1
The NM_080680.3(COL11A2):c.2220G>T(p.Glu740Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000036 in 1,612,908 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. E740E) has been classified as Likely benign.
Frequency
Consequence
NM_080680.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL11A2 | NM_080680.3 | c.2220G>T | p.Glu740Asp | missense_variant | 29/66 | ENST00000341947.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL11A2 | ENST00000341947.7 | c.2220G>T | p.Glu740Asp | missense_variant | 29/66 | 5 | NM_080680.3 | P4 | |
COL11A2 | ENST00000374708.8 | c.1962G>T | p.Glu654Asp | missense_variant | 27/64 | 5 | A1 | ||
COL11A2 | ENST00000361917.6 | c.795G>T | p.Glu265Asp | missense_variant | 16/24 | 5 | |||
COL11A2 | ENST00000477772.1 | n.272+945G>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152108Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000182 AC: 45AN: 246870Hom.: 1 AF XY: 0.000141 AC XY: 19AN XY: 134456
GnomAD4 exome AF: 0.0000370 AC: 54AN: 1460800Hom.: 1 Cov.: 35 AF XY: 0.0000275 AC XY: 20AN XY: 726714
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152108Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74290
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Mar 17, 2023 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at